Mass spectrometry is a highly robust method of analysis for peptides, proteins, nucleic acids and small molecules. However, there are some general guidelines that are important to remember for sample preparation when using mass spectrometry.The specific requirements for the methods of ionization will be covered briefly here. For a more thorough treatment of mass spectrometry methods and sample preparation, several general references are available.

J. Throck Watson, Introduction to Mass Spectrometry, 3rd Edition (1997), Lippincott-Raven, Philidelphia, PA.

Gary Siuzdak, The Expanding Role of Mass Spectrometry in Biotechnology - 2nd Edition (2006), MCC Press, San Diego, CA.

Michael Kinter and Nicholas E. Sherman, Protein Sequencing and Identification using Tandem Mass Spectrometry (2000), John Wiley and Sons, New York, NY.

     Salts are often problematic when using mass spectrometers. Because mass spectrometers identify the mass of a charged ion of an analyte molecule, excess salt can interfere with the performance of the mass spectrometer by overloading the system with charged salt ions. These salt ions can also assist in ionization and generate multiple salt adducts of the analyte. MALDI ionization is significantly more tolerant of salts in the sample than electrospray ionization. Metal salts such as those of sodium and potassium are usually more problematic than ammonium salts. For MALDI, metal salt concentrations of 100 millimolar are usually tolerated. In LC/MS, salts should be washed through the HPLC column prior to initiating a gradient for elution of the analyte molecules and starting mass spectral analysis.

     Detergents can severely affect the performance of mass spectrometers. The Triton series of detergents are well known and useful for many biological applications, but present serious problems when used in both MALDI and electrospray ionization methods. Mass spectrometers are more tolerant of detergents based on sugar moieties such as the N-octyl or –dodecylglucopyranosides. Please ask a member of the facility if you are unsure of your sample prep.

     The quantities of sample needed for mass spectrometry analysis are almost vanishingly small (on the order of 100 picomoles for the LC/MS system and femtomoles for the MALDI and LC/MS/MS systems). While some biological applications may require these limits, a more common problem within the facility has been utilizing high concentrations of samples. This has become a significant challenge with the Agilent LC/MS system. Overloading the mass spectrometers can result in contamination through subsequent samples, loss of sensitivity of the mass spectrometer and damage to the LC system. Users found to have damaged the instruments through abuse such as overloading will be charged for the necessary repairs.